With the latest thunderbird, the string to search for in the config editor to set it to check all folders for new email has changed from:

mail.check_all_imap_folders_for_new to mail.server.default.check_all_folders_for_new

As detailed here: http://kb.mozillazine.org/How_do_I_check_for_new_messages_in_other_folders Which caught me out for a while as I was looking for the old one in the config editor.